Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

diff plot_size_readmap.r @ 20:45df4c72a780 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 521b1e3fcf3dbf9d61d6b2b90d2415c3dadc4b5a
author drosofff
date Wed, 26 Sep 2018 11:06:34 -0400
parents be0c6b6466cc
children
line wrap: on
line diff
--- a/plot_size_readmap.r	Wed Dec 20 19:24:55 2017 -0500
+++ b/plot_size_readmap.r	Wed Sep 26 11:06:34 2018 -0400
@@ -99,7 +99,7 @@
 end=i+rows_per_page-1
 if (end>n_genes) {end=n_genes}
 if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
-readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange) , par.settings=par.settings.readmap)) }
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$yrange) , par.settings=par.settings.readmap)) }
 args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
                                     top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
                                     left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90)
@@ -131,7 +131,7 @@
 end=i+rows_per_page/2-1
 if (end>n_genes) {end=n_genes}
 if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
-readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange), par.settings=par.settings.readmap)) }
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$yrange), par.settings=par.settings.readmap)) }
 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
 plot.list=rbind(readmap_plot.list, size_plot.list )
 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
@@ -142,4 +142,4 @@
             )
 do.call(grid.arrange, args_list)
 }
-devname=dev.off()
\ No newline at end of file
+devname=dev.off()